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Genome Analysis Toolkit

Variant Discovery in High-Throughput Sequencing Data

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Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Learn more

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Show all All Planned Not planned Completed Answered No status Sort by recent activity Newest post Recent activity Votes Comments
  • SelectVariants error
    • Rajul Tayal
    • July 25, 2020 09:12
    • Edited
    0 votes 1 comment
  • WDL RNA-seq Hisat2
    • Thinh B. Vo
    • July 13, 2020 19:24
    0 votes 1 comment
  • Dosages with Mutect2
    • Leore Nehemie Bensabath
    • July 24, 2020 08:36
    0 votes 6 comments
  • RealignerTargetCreator
    • Madza Farias-Virgens
    • July 07, 2020 20:01
    0 votes 2 comments
  • Confusing GVCF results Answered
    • Yue Wang
    • July 07, 2020 14:31
    • Edited
    0 votes 1 comment
  • FilterMutectCalls failing filters
    • Elizabeth Schabot
    • July 13, 2020 20:57
    0 votes 1 comment
  • GATK mark duplicates error
    • Kshama Aswath
    • July 22, 2020 20:26
    • Edited
    0 votes 2 comments
  • FixVcfHeader error: A reference dictionary is required for creating Tribble indices on the fly
    • jorgez
    • July 20, 2020 18:52
    0 votes 10 comments
  • How to set the length when make a mask fasta file for Glycine_max.Glycine_max_v2.0.dna.fa
    • termius
    • July 17, 2020 08:45
    0 votes 2 comments
  • run SVPreprocess and SVGenotyper for each sample
    • zzq
    • July 16, 2020 04:10
    0 votes 7 comments
  • gatk3-register
    • touyupang
    • July 01, 2020 05:23
    0 votes 1 comment
  • Variable region not considered active region by HaplotypeCaller
    • Veronica
    • July 15, 2020 22:19
    0 votes 1 comment
  • How to execute workflow locally without docker
    • jiawei
    • July 11, 2020 15:28
    0 votes 1 comment
  • Picard LiftOverVCF 2.22.3. hs37d5_to_GRCh38. Many mismatched reference alleles
    • Argonaut44
    • June 23, 2020 18:09
    • Edited
    0 votes 3 comments
  • Extract individual samples from combined gvcf file
    • Balat
    • July 03, 2020 01:20
    0 votes 1 comment
  • SelectVariants to get a vcf file with 1 individual from a vcf file with 3 individuals
    • Linda Do
    • June 22, 2020 21:46
    0 votes 3 comments
  • Can't add to PATH
    • Linda Do
    • May 12, 2020 04:46
    0 votes 2 comments
  • Inquiry about the GATK Best Practices for variant calling on RNAseq
    • Benjamin Hing
    • July 02, 2020 00:24
    0 votes 1 comment
  • IlluminaBasecallsToSam - barcode was not expected
    • Vincent Hahaut
    • June 10, 2020 19:04
    0 votes 1 comment
  • copyright issue
    • Özlem Okutman
    • June 16, 2020 13:17
    0 votes 2 comments
  • What kind of statistical methods genome strip used?
    • zhangwusheng
    • February 19, 2020 18:21
    0 votes 3 comments
  • GenomicsDBImport does not recognize option --genomicsdb-update-workspace-path
    • Jose Luis Gualdron
    • June 08, 2020 08:08
    0 votes 2 comments
  • VariantRecalibrator throwing VariantRecalibratorEngine - Evaluate datum returned a NaN warning then crashing with empty tranches file.
    • David Murphy
    • June 02, 2020 12:58
    • Edited
    0 votes 2 comments
  • something wrong with MarkDuplicatesSpark
    • charles_cai
    • June 02, 2020 10:09
    0 votes 1 comment
  • LiftoverVcf fails to lift over a GVCF file. Error java.lang.ArrayIndexOutOfBoundsException: -1
    • jorgez
    • May 06, 2020 12:54
    0 votes 10 comments
  • resource bundle b37
    • hirokomatsui
    • June 19, 2020 00:20
    0 votes 1 comment
  • CombineGVCF slowing down at certain region on chromosome 1
    • wd
    • May 26, 2020 18:38
    • Edited
    0 votes 3 comments
  • Read counts in vcf files do not reflect local realignments
    • jhb
    • May 13, 2020 15:22
    • Edited
    0 votes 2 comments
  • Problem Installing and testing GATK-4.1.7.0
    • Arjun Upadhaya
    • May 04, 2020 06:34
    1 vote 5 comments
  • Genomestrip cannot find --ploidyMapFile
    • Swanthana Rekulapally
    • June 11, 2020 20:23
    0 votes 9 comments
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